I really like that my iLiad can follow internal links in pdfs and that I can create bookmarks in pdfs, but AFAIK it cannot yet follow the pdf bookmarks. So I wrote a bash script that extracts the pdf bookmarks and converts them into ipdf bookmarks that you can paste into manifest.xml. Run it with no arguments to get a list of options.

You would then replace the tag "<bookmarks/>" in manifest.xml with the contents of myfile.bookmarks.txt. Now when you read myfile.pdf on your iLiad, you can click the "sort" icon to access these bookmarks. (I'm not sure exactly what assumptions I'm making about what version of ipdf you're running.)

Since ipdf bookmarks cannot be nested, this script only picks out level 1 and level 2 bookmarks to avoid clutter, but you can use the -u and -l options to change this behavior.